Align Amino-acid permease RocE (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease
Query= SwissProt::P39137 (467 letters) >NCBI__GCF_002893965.1:WP_003943879.1 Length = 469 Score = 305 bits (780), Expect = 3e-87 Identities = 156/403 (38%), Positives = 246/403 (61%), Gaps = 8/403 (1%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 LQ T+K RHL MI++ GVIG G F+G+G I + GP G ++SY + G ++ L M LGE+ Sbjct: 9 LQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGP-GVLISYALAGVVVILVMRMLGEM 67 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 + A P +GSF +YA K I GF+ GWLY W + IE + +M RW P + W Sbjct: 68 SAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVPGVPQWT 127 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 W L+ ++ + N I+ K+F E EFWF+ IK++ I+ F+ +G A+ G + G +AP Sbjct: 128 WALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMP---GVEAPG 184 Query: 191 LTHFYEDGLF-PNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249 +T+ G F PNG AML ++ V F+F G E+ +AAGES +P + + ++K VWR Sbjct: 185 MTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSVVWRI 244 Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309 L+F++ SI V+ ++PW A V SP+VAV + GIP A +IM+ V+L ++LS NSGLY Sbjct: 245 LIFYIGSIAVVVTLLPWDSASVALSPYVAVMDSYGIPAAGNIMDVVVLTSVLSCLNSGLY 304 Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369 ++R+++++A G A K+L + + GVPM +++V+ V L++ + + V++ L++ Sbjct: 305 TASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLSPDKVFLFLVNS 364 Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVL 412 +G A W+ IS+SQ+ RRK G ++L+ K +P L Sbjct: 365 SGAIALFVWLVISVSQLRTRRKLEASG---QELELKMWFFPYL 404 Lambda K H 0.329 0.142 0.438 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 498 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 467 Length of database: 469 Length adjustment: 33 Effective length of query: 434 Effective length of database: 436 Effective search space: 189224 Effective search space used: 189224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory